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1. Species invasions shift microbial phenology in a two-decade freshwater time series

   https://doi.org/10.1073/pnas.2211796120  

   Rohwer, Robin R.; Hale, Riley J.; Vander Zanden, M. Jake; Miller, Todd R.; McMahon, Katherine D. (March 2023, Proceedings of the National Academy of Sciences)

   Invasive species impart abrupt changes on ecosystems, but their impacts on microbial communities are often overlooked. We paired a 20 y freshwater microbial community time series with zooplankton and phytoplankton counts, rich environmental data, and a 6 y cyanotoxin time series. We observed strong microbial phenological patterns that were disrupted by the invasions of spiny water flea ( Bythotrephes cederströmii ) and zebra mussels ( Dreissena polymorpha ). First, we detected shifts in Cyanobacteria phenology. After the spiny water flea invasion, Cyanobacteria dominance crept earlier into clearwater; and after the zebra mussel invasion, Cyanobacteria abundance crept even earlier into the diatom-dominated spring. During summer, the spiny water flea invasion sparked a cascade of shifting diversity where zooplankton diversity decreased and Cyanobacteria diversity increased. Second, we detected shifts in cyanotoxin phenology. After the zebra mussel invasion, microcystin increased in early summer and the duration of toxin production increased by over a month. Third, we observed shifts in heterotrophic bacteria phenology. The Bacteroidota phylum and members of the acI Nanopelagicales lineage were differentially more abundant. The proportion of the bacterial community that changed differed by season; spring and clearwater communities changed most following the spiny water flea invasion that lessened clearwater intensity, while summer communities changed least following the zebra mussel invasion despite the shifts in Cyanobacteria diversity and toxicity. A modeling framework identified the invasions as primary drivers of the observed phenological changes. These long-term invasion-mediated shifts in microbial phenology demonstrate the interconnectedness of microbes with the broader food web and their susceptibility to long-term environmental change. 

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2. Seasonal and interannual changes in a coastal Antarctic zooplankton community

   https://doi.org/10.3354/meps14256  

   Conroy, JA; Steinberg, DK; Thomas, MI; West, LT (February 2023, Marine Ecology Progress Series)

   Seasonal fluctuations are key features of high-latitude marine ecosystems, where zooplankton exhibit a wide array of adaptations within their life cycles. Repeated, sub-seasonal sampling of Antarctic zooplankton is rare, even along the West Antarctic Peninsula (WAP), where multidecadal changes in sea ice and phytoplankton are well documented. We quantified zooplankton biomass, size structure, and composition at 2 coastal time-series stations in the northern WAP over 3 field seasons (November-March) with different sea-ice, temperature, and phytoplankton conditions. Seasonal peaks in zooplankton biomass followed weeks after phytoplankton blooms. Biomass of mesozooplankton (0.2-2 mm) was consistent and low, while high biomass of macrozooplankton (>2 mm) occasionally resulted in a size distribution dominated by krill and salps, which appears to be a characteristic phenomenon of the Southern Ocean. Zooplankton composition and size changed between years and from spring to summer as the water column warmed after sea-ice breakup. Seasonal succession was apparent typically in decreasing zooplankton size and a shift to species that are less dependent upon phytoplankton. Mean central abundance dates varied by 54 d across 14 taxa, and specific feeding preferences and life-history traits explained the different seasonal abundance patterns. In all 3 yr, the dominant euphausiid species switched from Euphausia superba in spring to Thysanoessa macrura in late summer. Various taxa shifted their phenology between years in response to the timing of sea-ice breakup and the onset of phytoplankton productivity, a level of natural environmental variability to which they appear resilient. Nevertheless, the limits to this resilience in response to climate change remain uncertain. 

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3. Anoxia begets anoxia: A positive feedback to the deoxygenation of temperate lakes

   https://doi.org/10.1111/gcb.17046  

   Lewis, Abigail S.; Lau, Maximilian P.; Jane, Stephen F.; Rose, Kevin C.; Be'eri‐Shlevin, Yaron; Burnet, Sarah H.; Clayer, François; Feuchtmayr, Heidrun; Grossart, Hans‐Peter; Howard, Dexter W.; et al (January 2024, Global Change Biology)

   Abstract Declining oxygen concentrations in the deep waters of lakes worldwide pose a pressing environmental and societal challenge. Existing theory suggests that low deep‐water dissolved oxygen (DO) concentrations could trigger a positive feedback through which anoxia (i.e., very low DO) during a given summer begets increasingly severe occurrences of anoxia in following summers. Specifically, anoxic conditions can promote nutrient release from sediments, thereby stimulating phytoplankton growth, and subsequent phytoplankton decomposition can fuel heterotrophic respiration, resulting in increased spatial extent and duration of anoxia. However, while the individual relationships in this feedback are well established, to our knowledge, there has not been a systematic analysis within or across lakes that simultaneously demonstrates all of the mechanisms necessary to produce a positive feedback that reinforces anoxia. Here, we compiled data from 656 widespread temperate lakes and reservoirs to analyze the proposed anoxia begets anoxia feedback. Lakes in the dataset span a broad range of surface area (1–126,909 ha), maximum depth (6–370 m), and morphometry, with a median time‐series duration of 30 years at each lake. Using linear mixed models, we found support for each of the positive feedback relationships between anoxia, phosphorus concentrations, chlorophyllaconcentrations, and oxygen demand across the 656‐lake dataset. Likewise, we found further support for these relationships by analyzing time‐series data from individual lakes. Our results indicate that the strength of these feedback relationships may vary with lake‐specific characteristics: For example, we found that surface phosphorus concentrations were more positively associated with chlorophyllain high‐phosphorus lakes, and oxygen demand had a stronger influence on the extent of anoxia in deep lakes. Taken together, these results support the existence of a positive feedback that could magnify the effects of climate change and other anthropogenic pressures driving the development of anoxia in lakes around the world. 

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4. Time-series metagenomics reveals changing protistan ecology of a temperate dimictic lake

   https://doi.org/10.1186/s40168-024-01831-y  

   Krinos, Arianna I; Bowers, Robert M; Rohwer, Robin R; McMahon, Katherine D; Woyke, Tanja; Schulz, Frederik (December 2024, Microbiome)

   Abstract BackgroundProtists, single-celled eukaryotic organisms, are critical to food web ecology, contributing to primary productivity and connecting small bacteria and archaea to higher trophic levels. Lake Mendota is a large, eutrophic natural lake that is a Long-Term Ecological Research site and among the world’s best-studied freshwater systems. Metagenomic samples have been collected and shotgun sequenced from Lake Mendota for the last 20 years. Here, we analyze this comprehensive time series to infer changes to the structure and function of the protistan community and to hypothesize about their interactions with bacteria. ResultsBased on small subunit rRNA genes extracted from the metagenomes and metagenome-assembled genomes of microeukaryotes, we identify shifts in the eukaryotic phytoplankton community over time, which we predict to be a consequence of reduced zooplankton grazing pressures after the invasion of a invasive predator (the spiny water flea) to the lake. The metagenomic data also reveal the presence of the spiny water flea and the zebra mussel, a second invasive species to Lake Mendota, prior to their visual identification during routine monitoring. Furthermore, we use species co-occurrence and co-abundance analysis to connect the protistan community with bacterial taxa. Correlation analysis suggests that protists and bacteria may interact or respond similarly to environmental conditions. Cryptophytes declined in the second decade of the timeseries, while many alveolate groups (e.g., ciliates and dinoflagellates) and diatoms increased in abundance, changes that have implications for food web efficiency in Lake Mendota. ConclusionsWe demonstrate that metagenomic sequence-based community analysis can complement existing efforts to monitor protists in Lake Mendota based on microscopy-based count surveys. We observed patterns of seasonal abundance in microeukaryotes in Lake Mendota that corroborated expectations from other systems, including high abundance of cryptophytes in winter and diatoms in fall and spring, but with much higher resolution than previous surveys. Our study identified long-term changes in the abundance of eukaryotic microbes and provided context for the known establishment of an invasive species that catalyzes a trophic cascade involving protists. Our findings are important for decoding potential long-term consequences of human interventions, including invasive species introduction. 

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5. Whole-Ecosystem Experiments Reveal Varying Responses of Phytoplankton Functional Groups to Epilimnetic Mixing in a Eutrophic Reservoir

   https://doi.org/10.3390/w11020222  

   Lofton, Mary; McClure, Ryan; Chen, Shengyang; Little, John; Carey, Cayelan (February 2019, Water)

   Water column mixing can influence community composition of pelagic phytoplankton in lakes and reservoirs. Previous studies suggest that low mixing favors cyanobacteria, while increased mixing favors green algae and diatoms. However, this shift in community dominance is not consistently achieved when epilimnetic mixers are activated at the whole-ecosystem scale, possibly because phytoplankton community responses are mediated by mixing effects on other ecosystem processes. We conducted two epilimnetic mixing experiments in a small drinking water reservoir using a bubble-plume diffuser system. We measured physical, chemical, and biological variables before, during, and after mixing and compared the results to an unmixed reference reservoir. We observed significant increases in the biomass of cyanobacteria (from 0.8 ± 0.2 to 2.4 ± 1.1 μg L−1, p = 0.008), cryptophytes (from 0.7 ± 0.1 to 1.9 ± 0.6 μg L−1, p = 0.003), and green algae (from 3.8 to 4.4 μg L−1, p = 0.15) after our first mixing event, likely due to increased total phosphorus from entrainment of upstream sediments. After the second mixing event, phytoplankton biomass did not change but phytoplankton community composition shifted from taxa with filamentous morphology to smaller, rounder taxa. Our results suggest that whole-ecosystem dynamics and phytoplankton morphological traits should be considered when predicting phytoplankton community responses to epilimnetic mixing. 

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